Migrants rest inside a shelter after being rescued from boats at Lhoksukon in Indonesia's Aceh ProvinceRoni Bintang/Reuters

There has been a surge in refugees arriving from impoverished Bangladesh and Myanmar to Malaysia and Indonesia following a crackdown on trafficking by Thailand, usually the first destination in the region's people-smuggling network.

Chris Lewa, director of the non-profit Arakan Project, which has been monitoring boat departures and arrivals for more than a decade, estimates more than 100,000 men, women and children have boarded vessels since mid-2012.

Most are trying to reach Malaysia, but recent crackdowns on human trafficking networks have sent brokers and agents into hiding, making it impossible for migrants to disembark – in some cases even after family members have paid $2,000 (£1,280 or €1,779) or more for their release, she said.

Lewa believes up to 6,000 Rohingya and Bangaldeshis are still on boats in the Malacca Strait and nearby international waters. Tightly confined, and with limited access to food and clean water, their health is deteriorating, she said, adding that dozens of deaths have been reported.

A boat that carried Rohingya migrants for three months is seen at Langkawi islandOlivia Harris/ReutersThe hold of a boat that had been carrying Rohingya migrants for three monthsOlivia Harris/ReutersLiving quarters on a boat that had been carrying Rohingya migrants for three months is seen at Langkawi, MalaysiaOlivia Harris/ReutersA Malaysian Maritime Enforcement Agency official stands over the hold of a seized boat which had been carrying Rohingya and Bangladeshi migrants, at a naval base in LangkawiManan Vatsyayana/AFP

Four boats carrying nearly 600 people successfully landed in western Indonesia, with some migrants jumping into the water and swimming, but a fifth carrying hundreds more was turned away.

Indonesia's navy spokesman, First Adm. Manahan Simorangkir, said they were trying to go to Malaysia but got thrown off course. "We didn't intend to prevent them from entering our territory, but because their destination country was not Indonesia, we asked them to continue to the country where they actually want to go," he said.

Those who made it to shore aboard the other boats were taken to a sports stadium in Lhoksukon, the capital of North Aceh District, to be cared for and questioned, said Lt. Col. Achmadi, chief of police in the area.

Migrants rest on the floor of a shelter in Lhoksukon, Indonesia's Aceh ProvinceRoni Bintang/ReutersMigrants believed to be Rohingya sleep inside a shelter in Lhoksukon, Indonesia's Aceh ProvinceRoni Bintang/ReutersA Rohingya child is examined by a Malaysian medical team on Langkawi island, in Malaysia's northern state of KedahOlivia Harris/ReutersA Rohingya child is examined by a Malaysian nurse a day after landing at Pantai Pasir Berdengung beach in LangkawiOlivia Harris/ReutersA Rohingya child sleeps on pile of used clothes inside a shelter in Lhoksukon, Aceh province, IndonesiaUlet Ifansasti/Getty ImagesA Rohingya child peeps out of a doorway at a temporary detention centre in LangkawiManan Vatsyayana/AFP

"We had nothing to eat," said Rashid Ahmed, a 43-year-old Rohingya man who was on one of the boats. He said he left Myanmar's troubled state of Rakhine with his eldest son three months ago.

Muhammad Husein, one of those who landed in Indonesia, said the migrants were kept confined in the boats and given only small amounts of food and water. "We could see the land, we could see hills, but they would not let us off the boat," he said. "Many of us cried constantly but if we asked for water, we were beaten. They even beat the women."

He said his group and many other migrants were transferred to a bigger vessel and left adrift on the high seas. "We had to drink sea water and people just got sick. We kept looking for other boats. Finally [on Sunday] we saw lights that got brighter and brighter as we got closer. When we got close to land, some fishermen came and asked us where we were from. They called the [authorities] and we were told we are in Indonesia."

Police found a big wooden boat trapped in the sand in shallow waters at a beach of Langkawi, an island off Malaysia, and have since located 865 men, 101 women and 52 children, said Jamil Ahmed, the area's deputy police chief.

He added many appeared weak and thin and that at least two other boats have not been found.

Bangladeshi migrants wait at the police headquarters in Langkawi after landing on Malaysian shoresManan Vatsyayana/AFPBangladeshi migrant Jahangir Hussain looks out of a police van at the police headquarters in LangkawiManan Vatsyayana/AFPMd Shafiqual shows his Bangladeshi identification card at the police headquarters in Langkawi, MalaysiaManan Vatsyayana/AFP

One Rohingya refugee, Pronmina, said there were hundreds on her boat alone. "We had to walk in Maungdaw [in Rakhine State, Myanmar] for one night to cross to Bangladesh by rowing boat and then we floated for three months," Pronmina added, when asked how she got to Malaysia.

Attacks on members of the religious minority, numbering around 1.3 million, have in the past three years left up to 280 people dead and forced 140,000 others from their homes. They now live under apartheid-like conditions in crowded camps just outside the Rakhine state capital, Sittwe, where they have little access to school or adequate health care.

The conditions at home – and lack of job opportunities – have sparked one of the biggest exoduses of boat people since the Vietnam War.

Samsidah Begom binti Abdul Syukur cries as she makes a phone call to her son in Malaysia from a shelter in Lhoksukon, Aceh province, IndonesiaUlet Ifansasti/Getty ImagesA young Rohingya boy waits along with other migrants at a temporary detention centre in LangkawiManan Vatsyayana/AFP

Rohingya packing into ships in the Bay of Bengal have been joined in growing numbers by Bangladeshis fleeing poverty and hoping to find a better life elsewhere.

Up until recently, their first stop was Thailand, where they were held in open pens in jungle camps as brokers collected "ransoms" from relatives. Those who could pay continued onward, usually to Malaysia or other countries. Those who couldn't were sometimes beaten, killed or left to die.

Since 1 May, police have unearthed two dozen bodies from shallow graves in the mountains of southern Thailand, the apparent victims of smuggling rings.

Human remains are retrieved from a mass grave at a rubber plantation in Thailand's southern Songkhla provinceSurapan Boonthanom/ReutersPolicemen take notes behind human remains retrieved from a mass grave at a rubber plantation near a mountain in Thailand's southern Songkhla provinceSurapan Boonthamon/ReutersRescue workers transport one of the bodies found at an abandoned camp in Thailand's southern Songkhla provinceSurapan Boonthamon/Reuters

The Bangkok Post reported that about 250 refugees have been found wandering around in the jungle-covered area of southern Thailand near the border with Malaysia over the past week, apparently people who were abandoned by smugglers.

Migrants from Myanmar and Bangladesh rest at Rattaphum district hall in Thailand's southern Songkhla provinceSurapan Boonthanom/ReutersRohingya migrant Muhammad Solim, 20, sits in a house in Nakhon Si Thammarat province, Thailand. He said he suffers from the effects of malnutrition after spending nearly three months at sea and 90 days in a jungle camp before he was ransomedAubrey Belford/Reuters